Package com.biomatters.geneious.publicapi.documents.sequence

Class DefaultNucleotideGraph

java.lang.Object

com.biomatters.geneious.publicapi.documents.sequence.DefaultNucleotideGraph

All Implemented Interfaces:

ExtendedNucleotideGraph, NucleotideGraph

public final class DefaultNucleotideGraph
extends Object
implements ExtendedNucleotideGraph

A NucleotideGraph that stores its values in int[] arrays internally, and allows getting and setting those arrays.

Nested Class Summary

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideGraph

NucleotideGraph.ImmutableGraphProvider

Field Summary

Fields

Modifier and Type	Field	Description
static final int	EDITED_NUCLEOTIDE_QUALITY	The quality score assigned to a nucleotide which is edited in a sequence with quality.

Constructor Summary

Constructors

Constructor	Description
DefaultNucleotideGraph(int[][] chromatogramValues, int[] chromatogramPositionsForResidues, int[] sequenceQualities, int sequenceLength, int chromatogramLength)	Construct a new DefaultNucleotideGraph.

Method Summary

Modifier and Type	Method	Description
static DefaultNucleotideGraph	copyOf(NucleotideGraph graph)	Creates a copy of the given graph.
static ExtendedNucleotideGraph	createGraphWithAdjustedEndGaps(ExtendedNucleotideGraph originalGraph, int newLeadingGapsLength, int newTrailingGapsLength)	Creates a copy of the given graph with the length of its end gaps adjusted.
static NucleotideGraph	createNucleotideGraph(int[][] chromatogramValues, int[] chromatogramPositionsForResidues, int[] sequenceQualities, int sequenceLength, int chromatogramLength)	Creates a new nucleotide graph.
static NucleotideGraph	createNucleotideGraph(int[][] chromatogramValues, int[] chromatogramPositionsForResidues, int[] sequenceQualities, int sequenceLength, int chromatogramLength, int leadingGapsLength, int trailingGapsLength)	Creates a new nucleotide graph.
static NucleotideGraph	createNucleotideGraph(int[] internalQualities, int leadingGapsLength, int trailingGapsLength)	Creates a new nucleotide graph with qualities but no traces.
static NucleotideGraph	createNucleotideGraph(NucleotideGraph graphToCopy)	Creates a deep copy of the given graph.
static ExtendedNucleotideGraph	createNucleotideGraphAdjustedForGapInsertion(NucleotideGraph graphToCopy, CharSequence charSequence)	Creates a deep copy of the given graph with all graph values adjusted to compensate for gap insertion as indicated by the presense of gaps in charSequence.
int	getChromatogramLength()	The number of points for which this graph has values, which is typically larger than the length of the nucleotide sequence because a base isn't called at every position in the graph.
int	getChromatogramPositionForResidue(int residueIndex)	The graph position (can be used as an argument to NucleotideGraph.getChromatogramValue(int, int)) where the nucleotide at the specified residue index has been called.
int[]	getChromatogramPositionsForResidues(int startIndex, int endIndex)
static int[]	getChromatogramPositionsForResidues(NucleotideGraph graph)	Equivalent to calling getChromatogramPositionsForResidues(graph,0,graph.getSequenceLength())
static int[]	getChromatogramPositionsForResidues(NucleotideGraph graph, int startIndex, int endIndex)	Get all the values returned from NucleotideGraph.getChromatogramPositionForResidue(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive).
int	getChromatogramValue(int nucleotideStateNumber, int graphPosition)	Returns the graph value for the specified nucleotide and at the specified position.
int[]	getChromatogramValues(int nucleotideStateNumber)
static int[][]	getChromatogramValues(NucleotideGraph graph)
static int[]	getChromatogramValues(NucleotideGraph graph, int i)
DefaultNucleotideGraph	getGraphAdjustedForDeletion(int firstResidueIndex, int lastResidueIndexExclusive, SequenceCharSequence newCharSequence)	Returns a new graph equivalent to this one, but adjusted to take into account a deletion from the associated sequence.
DefaultNucleotideGraph	getGraphAdjustedForInsertion(int residueIndex, CharSequence insertedChars)	Returns a new graph equivalent to this one, but adjusted to take into account an insertion into the associated sequence.
ExtendedNucleotideGraph	getGraphAdjustedForReplacement(int residueIndex, int numberOfResiduesReplaced)	Returns a new graph equivalent to this one, but with quality scores in the replaced nucleotides adjusted to be EDITED_NUCLEOTIDE_QUALITY
int	getLeadingGapsLength()	Get the number of leading residues in the sequence this graph corresponds to that are all gaps.
int	getSequenceLength()	The length of the nucleotide sequence that can be annotated with this graph.
int[]	getSequenceQualities(int startIndex, int endIndex)
static int[]	getSequenceQualities(NucleotideGraph graph)	Equivalent to calling getSequenceQualities(graph,0,graph.getSequenceLength())
static int[]	getSequenceQualities(NucleotideGraph graph, int startIndex, int endIndex)	Get all the values returned from NucleotideGraph.getSequenceQuality(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive).
int	getSequenceQuality(int residueIndex)	Returns a measurement of confidence in the residue reported at the specified residueIndex in the sequence.
int	getTrailingGapsLength()	Get the number of trailing residues in the sequence this graph corresponds to that are all gaps.
boolean	hasChromatogramPositionsForResidues()	Tests whether this NucleotideGraph contains information about the position of the base calls, i.e.
boolean	hasChromatogramValues(int nucleotideStateNumber)	Specifies whether it is legal to call NucleotideGraph.getChromatogramValue(int, int) for the specified nucleotide.
boolean	hasSequenceQualities()	Tests whether this graph contains information about the confidence in the associated sequence's residues, i.e.
static ExtendedNucleotideGraph	readObject(GeneiousObjectInputStream in)	Reads a graph previously written using writeObject(GeneiousObjectOutputStream, NucleotideGraph)
static ExtendedNucleotideGraph	readObject(DataInput in)	Reads a graph previously written using writeObject(java.io.DataOutput, NucleotideGraph)
static ExtendedNucleotideGraph	reverseComplement(NucleotideGraph graphToReverseComplement)	Creates a new graph that is the reverse complement of the given graph.
DefaultNucleotideGraph	setChromatogramPositionsForResidues(int[] newSitePositions)
DefaultNucleotideGraph	setChromatogramValues(int[][] newGraphValues)
DefaultNucleotideGraph	setSequenceQualities(int[] newQualities)
static void	writeObject(GeneiousObjectOutputStream out, NucleotideGraph graph)	Writes the given graph in a binary format to an output stream (as specified by Serializable) such that it can be recreated using readObject(GeneiousObjectInputStream).
static void	writeObject(Geneious.MajorVersion version, DataOutput out, NucleotideGraph graph)	Writes the given graph in a binary format to an output stream (as specified by Serializable) such that it can be recreated using readObject(java.io.DataInput).
static void	writeObject(DataOutput out, NucleotideGraph graph)	Equivalent to writeObject(Geneious.getMajorVersion(), out, graph)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

EDITED_NUCLEOTIDE_QUALITY

public static final int EDITED_NUCLEOTIDE_QUALITY

The quality score assigned to a nucleotide which is edited in a sequence with quality. This has a value of 63, which is higher than any quality score assigned by a Sanger machine and can therefore be used by consensus calling to know not to further inspect the trace to make a call, but instead respect what the user has assigned for the base call.

Since:

API 4.201910

See Also:

• Constant Field Values

Constructor Details

DefaultNucleotideGraph

public DefaultNucleotideGraph(int[][] chromatogramValues,
 int[] chromatogramPositionsForResidues,
 int[] sequenceQualities,
 int sequenceLength,
 int chromatogramLength)

Construct a new DefaultNucleotideGraph. It is generally preferable to use createNucleotideGraph(int[][], int[], int[], int, int) instead unless you require the returned graph to be a DefaultNucleotideGraph rather than just a NucleotideGraph.

Method Details

getLeadingGapsLength

public int getLeadingGapsLength()

Description copied from interface: ExtendedNucleotideGraph

Get the number of leading residues in the sequence this graph corresponds to that are all gaps. NucleotideGraph.getSequenceQuality(int) and NucleotideGraph.getChromatogramPositionForResidue(int) will both return Integer.MIN_VALUE for residueIndices less than the number of leading gaps.

Note, an implementation may choose to return 0 from this method even if it has leading end gaps or any value less than or equal to the number of leading gaps it has.

Specified by:

getLeadingGapsLength in interface ExtendedNucleotideGraph

Returns:

the number of leading residues in the sequence this graph corresponds to that are all gaps.

getTrailingGapsLength

public int getTrailingGapsLength()

Description copied from interface: ExtendedNucleotideGraph

Get the number of trailing residues in the sequence this graph corresponds to that are all gaps. NucleotideGraph.getSequenceQuality(int) and NucleotideGraph.getChromatogramPositionForResidue(int) will both return Integer.MIN_VALUE for residueIndices within this much of NucleotideGraph.getSequenceLength().

Note, an implementation may choose to return 0 from this method even if it has trailing end gaps or any value less than or equal to the number of trailing gaps it has.

Specified by:

getTrailingGapsLength in interface ExtendedNucleotideGraph

Returns:

the number of trailing residues in the sequence this graph corresponds to that are all gaps.

getChromatogramValues

public static int[][] getChromatogramValues(NucleotideGraph graph)

getChromatogramValues

public static int[] getChromatogramValues(NucleotideGraph graph,
 int i)

getChromatogramPositionsForResidues

public static int[] getChromatogramPositionsForResidues(NucleotideGraph graph)

Equivalent to calling getChromatogramPositionsForResidues(graph,0,graph.getSequenceLength())

getChromatogramPositionsForResidues

public static int[] getChromatogramPositionsForResidues(NucleotideGraph graph,
 int startIndex,
 int endIndex)

Get all the values returned from NucleotideGraph.getChromatogramPositionForResidue(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive).

Returns:

all the values returned from NucleotideGraph.getChromatogramPositionForResidue(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive) or null if NucleotideGraph.hasChromatogramPositionsForResidues()==false.

getChromatogramPositionsForResidues

public int[] getChromatogramPositionsForResidues(int startIndex,
 int endIndex)

Specified by:

getChromatogramPositionsForResidues in interface NucleotideGraph

Parameters:

startIndex - the 0-based start residue index (inclusive)

endIndex - the 0-based end residue index (exclusive)

Returns:

all the values returned from NucleotideGraph.getChromatogramPositionForResidue(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive) or null if NucleotideGraph.hasChromatogramPositionsForResidues()==false.

getSequenceQualities

public static int[] getSequenceQualities(NucleotideGraph graph)

Equivalent to calling getSequenceQualities(graph,0,graph.getSequenceLength())

getSequenceQualities

public static int[] getSequenceQualities(NucleotideGraph graph,
 int startIndex,
 int endIndex)

Get all the values returned from NucleotideGraph.getSequenceQuality(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive).

Returns:

all the values returned from NucleotideGraph.getSequenceQuality(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive) or null if NucleotideGraph.hasSequenceQualities()==false.

getSequenceQualities

public int[] getSequenceQualities(int startIndex,
 int endIndex)

Specified by:

getSequenceQualities in interface NucleotideGraph

Parameters:

startIndex - the 0-based start residue index (inclusive)

endIndex - the 0-based end residue index (exclusive)

Returns:

all the values returned from NucleotideGraph.getSequenceQuality(int) for all residues indices in the range startIndex (inclusive) to endIndex (exclusive) or null if NucleotideGraph.hasSequenceQualities()==false.

getChromatogramValues

public int[] getChromatogramValues(int nucleotideStateNumber)

Specified by:

getChromatogramValues in interface NucleotideGraph

Parameters:

nucleotideStateNumber - The nucleotide for which to retrieve the graph value, encoded as 0 = A, 1 = C, 2 = G, 3 = T (alphabetic order, same as in Nucleotides)

Returns:

all the values returned from NucleotideGraph.getChromatogramValue(int, int) for this nucleotideStateNumber for all indices in the range 0 to NucleotideGraph.getChromatogramLength() (exclusive) or null if NucleotideGraph.hasChromatogramValues(int)==false for this nucleotideStateNumber.

setSequenceQualities

public DefaultNucleotideGraph setSequenceQualities(int[] newQualities)

setChromatogramPositionsForResidues

public DefaultNucleotideGraph setChromatogramPositionsForResidues(int[] newSitePositions)

setChromatogramValues

public DefaultNucleotideGraph setChromatogramValues(int[][] newGraphValues)

createNucleotideGraph

public static NucleotideGraph createNucleotideGraph(int[][] chromatogramValues,
 int[] chromatogramPositionsForResidues,
 int[] sequenceQualities,
 int sequenceLength,
 int chromatogramLength,
 int leadingGapsLength,
 int trailingGapsLength)

Creates a new nucleotide graph. This method always returns an ExtendedNucleotideGraph but is declared to return a NucleotideGraph for backwards compatilbity reasons.

Parameters:

chromatogramValues - the values to be returned from getChromatogramValue(int, int). May be null.

chromatogramPositionsForResidues - the values to be returned from getChromatogramPositionForResidue(int) . May be null.

sequenceQualities - the values to be returned from getSequenceQualities(NucleotideGraph). May be null. The quality values must not include those in end gap regions (specified by leadingGapsLength and trailingGapsLength)

sequenceLength - the value to return from getSequenceLength()

chromatogramLength - the value to return from getChromatogramLength()

leadingGapsLength - the number of leading gaps in the sequence. chromatogramPositionsForResidues and sequenceQualities do not need to cover the leading gaps regions

trailingGapsLength - the number of leading gaps in the sequence. chromatogramPositionsForResidues and sequenceQualities do not need to cover the leading gaps regions

Returns:

the new graph.

createNucleotideGraph

public static NucleotideGraph createNucleotideGraph(int[] internalQualities,
 int leadingGapsLength,
 int trailingGapsLength)

Creates a new nucleotide graph with qualities but no traces.

Parameters:

internalQualities - the values to be returned from getSequenceQualities(NucleotideGraph). The quality values must not include those in end gap regions (specified by leadingGapsLength and trailingGapsLength)

leadingGapsLength - leading gaps length

trailingGapsLength - trailing gaps length

Returns:

the new graph

Since:

API 4.50 (Geneious 5.5.0)

createNucleotideGraph

public static NucleotideGraph createNucleotideGraph(int[][] chromatogramValues,
 int[] chromatogramPositionsForResidues,
 int[] sequenceQualities,
 int sequenceLength,
 int chromatogramLength)

Creates a new nucleotide graph. This method always returns an ExtendedNucleotideGraph but is declared to return a NucleotideGraph for backwards compatilbity reasons.

Parameters:

chromatogramValues - the values to be returned from getChromatogramValue(int, int). May be null.

chromatogramPositionsForResidues - the values to be returned from getChromatogramPositionForResidue(int) . May be null.

sequenceQualities - the values to be returned from getSequenceQualities(NucleotideGraph). May be null. The quality values must not include those in end gap regions (specified by leadingGapsLength and trailingGapsLength)

sequenceLength - the value to return from getSequenceLength()

chromatogramLength - the value to return from getChromatogramLength()

Returns:

the new graph.

createNucleotideGraphAdjustedForGapInsertion

public static ExtendedNucleotideGraph createNucleotideGraphAdjustedForGapInsertion(NucleotideGraph graphToCopy,
 CharSequence charSequence)

Creates a deep copy of the given graph with all graph values adjusted to compensate for gap insertion as indicated by the presense of gaps in charSequence.

Parameters:

graphToCopy - the graph to copy

charSequence - a CharSequence used for determining the positions of gaps to insert into the graph.

Returns:

a deep copy of the graph adjusted for gap insertion

reverseComplement

public static ExtendedNucleotideGraph reverseComplement(NucleotideGraph graphToReverseComplement)

Creates a new graph that is the reverse complement of the given graph.

Parameters:

graphToReverseComplement - the graph to reverse complement

Returns:

a newly created graph which is the reverse complement of the given graph.

createNucleotideGraph

public static NucleotideGraph createNucleotideGraph(NucleotideGraph graphToCopy)

Creates a deep copy of the given graph. This method always returns an ExtendedNucleotideGraph but is declared to return a NucleotideGraph for backwards compatilbity reasons.

Parameters:

graphToCopy - the graph to copy

Returns:

a deep copy of the graph.

createGraphWithAdjustedEndGaps

public static ExtendedNucleotideGraph createGraphWithAdjustedEndGaps(ExtendedNucleotideGraph originalGraph,
 int newLeadingGapsLength,
 int newTrailingGapsLength)

Creates a copy of the given graph with the length of its end gaps adjusted. If the original graph was created using one of the createNucleotideGraph methods in this class, then this method will be efficient in that the actual graph data can be resued in the returned class since original graph is immutable.

Parameters:

originalGraph - the graph to create a copy of

newLeadingGapsLength - the length of the leading gaps in the returned graph

newTrailingGapsLength - the length of the trailing gaps in the returned graph

Returns:

a new graph

copyOf

public static DefaultNucleotideGraph copyOf(NucleotideGraph graph)

Creates a copy of the given graph. It is generally preferable to use createNucleotideGraph(NucleotideGraph) instead unless you require the returned graph to be a DefaultNucleotideGraph rather than just a NucleotideGraph.

Parameters:

graph - the graph to copy

Returns:

a copy of the graph

getChromatogramLength

public int getChromatogramLength()

Description copied from interface: NucleotideGraph

The number of points for which this graph has values, which is typically larger than the length of the nucleotide sequence because a base isn't called at every position in the graph.

Specified by:

getChromatogramLength in interface NucleotideGraph

Returns:

the length of this graph, or 0 if this graph has no graph values for any nucleotide (i.e. 0 if NucleotideGraph.hasChromatogramPositionsForResidues() is false).

getChromatogramValue

public int getChromatogramValue(int nucleotideStateNumber,
 int graphPosition)
                         throws IndexOutOfBoundsException

Description copied from interface: NucleotideGraph

Returns the graph value for the specified nucleotide and at the specified position. If the graph is a chromatogram, this is a measure of the support for the specified nucleotide at this position. May only be called if NucleotideGraph.hasChromatogramValues(int) returns true for the specified nucleotide.

Specified by:

getChromatogramValue in interface NucleotideGraph

Parameters:

nucleotideStateNumber - The nucleotide for which to retrieve the graph value, encoded as 0 = A, 1 = C, 2 = G, 3 = T (alphabetic order, same as in Nucleotides)

graphPosition - The position in the sequence for which to query the graph value, with 0 <= graphPosition < graph length

Returns:

the graph value for the specified nucleotide and at the specified position.

Throws:

IndexOutOfBoundsException - if graphPosition < 0 or graphPosition >= NucleotideGraph.getChromatogramLength()

hasChromatogramValues

public boolean hasChromatogramValues(int nucleotideStateNumber)

Description copied from interface: NucleotideGraph

Specifies whether it is legal to call NucleotideGraph.getChromatogramValue(int, int) for the specified nucleotide.

Specified by:

hasChromatogramValues in interface NucleotideGraph

Parameters:

nucleotideStateNumber - A nucleotide state number encoded in the same way as for NucleotideGraph.getChromatogramValue(int, int), i.e. 0 = A, 1 = C, 2 = G, 3 = T

Returns:

true if is legal to call NucleotideGraph.getChromatogramValue(int, int) for the specified nucleotide

getSequenceLength

public int getSequenceLength()

Description copied from interface: NucleotideGraph

The length of the nucleotide sequence that can be annotated with this graph. If a class implements both this interface and SequenceDocument, then the return value of this method must be equal to getCharSequence().length() Also if NucleotideGraph.hasChromatogramPositionsForResidues() or NucleotideGraph.hasSequenceQualities() is true, the return value indicates the range of legal values to pass to NucleotideGraph.getChromatogramPositionForResidue(int) and NucleotideGraph.getSequenceQuality(int).

Specified by:

getSequenceLength in interface NucleotideGraph

Returns:

length of the nucleotide sequence belonging to this graph.

getChromatogramPositionForResidue

public int getChromatogramPositionForResidue(int residueIndex)
                                      throws IndexOutOfBoundsException,
UnsupportedOperationException

Description copied from interface: NucleotideGraph

The graph position (can be used as an argument to NucleotideGraph.getChromatogramValue(int, int)) where the nucleotide at the specified residue index has been called. This method may only be called if NucleotideGraph.hasChromatogramPositionsForResidues() returns true. The graph sites are guaranteed to have the same order as the sequence nucleotides. Therefore, any implementation must ensure that if i < j, then getChromatogramPositionForResidue(i) <= getChromatogramPositionForResidue(j).

Specified by:

getChromatogramPositionForResidue in interface NucleotideGraph

Parameters:

residueIndex - A value 0 <= residueIndex < NucleotideGraph.getSequenceLength() specifying the index in the nucleotide sequence for which to calculate the corresponding position in the graph.

Returns:

A value in the range 0 <= value < NucleotideGraph.getChromatogramLength(), specifiying the graph position where the nucleotide that is at position residueIndex has been called. For positions residueIndex where the sequence length consisting of values between 0 and getChromatogramLength()-1 inclusive. For a residueIndex where the sequence holds a '-', the returned site position must always be Integer.MIN_VALUE.

Throws:

IndexOutOfBoundsException - if residueIndex invalid input: '<' 0 or residueIndex > NucleotideGraph.getSequenceLength().

UnsupportedOperationException - if !hasChromatogramPositionsForResidues().

hasChromatogramPositionsForResidues

public boolean hasChromatogramPositionsForResidues()

Description copied from interface: NucleotideGraph

Tests whether this NucleotideGraph contains information about the position of the base calls, i.e. whether it is legal to call NucleotideGraph.getChromatogramPositionForResidue(int).

Specified by:

hasChromatogramPositionsForResidues in interface NucleotideGraph

Returns:

true if this NucleotideGraph contains information about the position of the base calls.

getSequenceQuality

public int getSequenceQuality(int residueIndex)
                       throws IndexOutOfBoundsException,
UnsupportedOperationException

Description copied from interface: NucleotideGraph

Returns a measurement of confidence in the residue reported at the specified residueIndex in the sequence. The measure is on a logaritmic scale: P(call correct) = 1 - 10^(-v/10) where v is the quality returned from this method.

If the sequence contains a gap at the specified position, this method should return Integer.MIN_VALUE if it is an end gap. If it is an internal gap, it should return the average quality of the non-gap positions on either side of the gap.

This method may only be called if NucleotideGraph.hasSequenceQualities() returns true.

Specified by:

getSequenceQuality in interface NucleotideGraph

Parameters:

residueIndex - A value 0 <= residueIndex < NucleotideGraph.getSequenceLength() specifying the index in the nucleotide sequence for which to calculate the quality of the graph.

Returns:

The quality score v for the residue at the specified index in the nucleotide sequence, which indicates the reliability of the nucleotide on a logarithmic scale as described above. For all positions other than end-gaps, this must be non-negative (since below 0 would imply a negative probability)

Throws:

IndexOutOfBoundsException - if residueIndex invalid input: '<' 0 or residueIndex > NucleotideGraph.getSequenceLength().

UnsupportedOperationException - if !hasSequenceQualities().

hasSequenceQualities

public boolean hasSequenceQualities()

Description copied from interface: NucleotideGraph

Tests whether this graph contains information about the confidence in the associated sequence's residues, i.e. whether it is legal to call NucleotideGraph.getSequenceQuality(int).

Specified by:

hasSequenceQualities in interface NucleotideGraph

Returns:

true if it is legal to call NucleotideGraph.getSequenceQuality(int) on this graph.

writeObject

public static void writeObject(GeneiousObjectOutputStream out,
 NucleotideGraph graph)
                        throws IOException

Writes the given graph in a binary format to an output stream (as specified by Serializable) such that it can be recreated using readObject(GeneiousObjectInputStream). Note, if the given graph is not a standard NucleotideGraph implementation (one created by createNucleotideGraph(NucleotideGraph)), then the object read back in will be converted to a standard NucleotideGraph implementation.

Parameters:

out - the stream to write to.

graph - the graph to write to the stream

Throws:

IOException - if it cannot be written to the stream.

writeObject

public static void writeObject(DataOutput out,
 NucleotideGraph graph)
                        throws IOException

Equivalent to writeObject(Geneious.getMajorVersion(), out, graph)

Parameters:

out - the stream to write to. If out is not a GeneiousObjectOutputStream and the graph is an ImmutableSequence its name may be uncompacted during deserialization

graph - the graph to write to the stream

Throws:

IOException - if it cannot be written to the stream.

Since:

API 4.30 (Geneious 5.3.0)

writeObject

public static void writeObject(Geneious.MajorVersion version,
 DataOutput out,
 NucleotideGraph graph)
                        throws IOException

Writes the given graph in a binary format to an output stream (as specified by Serializable) such that it can be recreated using readObject(java.io.DataInput). Note, if the given graph is not a standard NucleotideGraph implementation (one created by createNucleotideGraph(NucleotideGraph)), then the object read back in will be converted to a standard NucleotideGraph implementation.

Parameters:

version - the Geneious version to ensure the data is compatible with

out - the stream to write to. If out is not a GeneiousObjectOutputStream and the graph is an ImmutableSequence its name may be uncompacted during deserialization

graph - the graph to write to the stream

Throws:

IOException - if it cannot be written to the stream.

Since:

API 4.600 (Geneious 6.0.0)

readObject

public static ExtendedNucleotideGraph readObject(GeneiousObjectInputStream in)
                                          throws IOException

Reads a graph previously written using writeObject(GeneiousObjectOutputStream, NucleotideGraph)

Parameters:

in - the stream to read from

Returns:

the graph read from the stream

Throws:

IOException - if it cannot be read from the stream.

readObject

public static ExtendedNucleotideGraph readObject(DataInput in)
                                          throws IOException

Reads a graph previously written using writeObject(java.io.DataOutput, NucleotideGraph)

Parameters:

in - the stream to read from

Returns:

the graph read from the stream

Throws:

IOException - if it cannot be read from the stream.

Since:

API 4.30 (Geneious 5.3.0)

getGraphAdjustedForReplacement

public ExtendedNucleotideGraph getGraphAdjustedForReplacement(int residueIndex,
 int numberOfResiduesReplaced)

Returns a new graph equivalent to this one, but with quality scores in the replaced nucleotides adjusted to be EDITED_NUCLEOTIDE_QUALITY

Parameters:

residueIndex - the first (zero based) position of a replaced nucleotide

numberOfResiduesReplaced - the number of nucleotides replaced

Returns:

a new graph, or this graph if no nucleotides were replaced.

Since:

API 4.201910

getGraphAdjustedForInsertion

public DefaultNucleotideGraph getGraphAdjustedForInsertion(int residueIndex,
 CharSequence insertedChars)

Returns a new graph equivalent to this one, but adjusted to take into account an insertion into the associated sequence.

Parameters:

residueIndex - the 0-based index to insert the new sequence at

insertedChars - the newly inserted characters.

Returns:

a new graph equivalent to this one, but adjusted to take into account an insertion into the associated sequence or this graph if no changes were needed.

Since:

API 4.700 (Geneious 7.0.0)

getGraphAdjustedForDeletion

public DefaultNucleotideGraph getGraphAdjustedForDeletion(int firstResidueIndex,
 int lastResidueIndexExclusive,
 SequenceCharSequence newCharSequence)

Returns a new graph equivalent to this one, but adjusted to take into account a deletion from the associated sequence.

Parameters:

firstResidueIndex - the 0-based index to begin the deletion from

lastResidueIndexExclusive - the 0-based index (exclusive) to finish the deletion at

newCharSequence - required if the leading and trailing gaps of the result are to be correct. (in case we delete all bases between and end gap and an internal gap then the end gaps need to be incremented). May be null if the calling code doesn't care if the leading and end gaps might be not as high as they should be

Returns:

a new graph equivalent to this one, but adjusted to take into account a deletion from the associated sequence or this graph if no changes were needed.

Since:

API 4.700 (Geneious 7.0.0)